The problem is simple: both men are Senators in states where you cannot run for two federal positions at the same time. The answer is equally simple: neither should run for President in 2016. Rand Paul should stay in the Senate and be an awesomely cranky Senate Majority Leader*; and Marco Rubio should run for governor of Florida in 2018 and get ready for 2024.
There. Problems solved. That should have cost each Senator five thousand dollars apiece in consulting fees, but apparently those jobs are all locked up already.
*Seriously, there’s all sorts of things that you can do to a federal bureaucracy from the top.